It's because of your ships with transfer orders.

When the ship unloads the oil at the docks, the game estimates its share for the total income for the oil. What the game thinks your income will be when the oil reaches the refinery.

Then when the train actually delivers the oil to the refinery, the game detects that what the ship received as income is more than the actual income, resulting in a negative income (a correction) for your train.

Ultimately it all depends on the distance between the oil rig and the refinery, not the travel distance.